In many catchments, lakes and streams are hydrologically linked in spatial patterns that influence nutrient transport, temperatures, and biogeochemical processes. Lakes may affect nutrient transport down-catchment in two ways: thermal enrichment, where warm lake outflows have high epilithic biomass and high nutrient demand; and nutrient removal, where lakes represent a sink for inorganic nutrients and exacerbate nutrient limitation downstream. To better understand interactions between streams and lakes, we measured biogeochemical structure and function along three watersheds that had varying numbers of lakes in the Sawtooth Mountains, Idaho. Both mechanisms were supported by our data. In all watersheds, inflow streams generally had higher concentrations of inorganic N and P than outflow streams, and outflow streams had higher epilithic biomass. Nitrate and phosphate uptake lengths in lake inflows were 2X higher than lake outflows, suggesting that outflow streams were more nutrient limited. Catchments with few lakes exhibited 25% less nutrient retention overall than a catchment with many lakes, further supporting our hypotheses. Our results highlight the importance of understanding stream-lake linkages in predicting catchment scale nutrient transport and retention.